From owner-chemistry@ccl.net Thu Jan 10 07:12:00 2013 From: "Martin Bohl martin],[moldiscovery.com" To: CCL Subject: CCL: MoKa 2.0 software for pKa and tautomer modelling Message-Id: <-48051-130110070111-19336-QluyFHLPkH394n21KjIFWQ.:.server.ccl.net> X-Original-From: "Martin Bohl" Date: Thu, 10 Jan 2013 07:01:10 -0500 Sent to CCL by: "Martin Bohl" [martin##moldiscovery.com] Dear Colleagues, We would like to draw your attention to the new release of the MoKa 2.0 software. As you know, the accurate prediction of a molecule's pKa and tautomeric state is critical to the accurate prediction of many important molecular properties, including solubility, site and rate of metabolism, permeation, lipophilicity, and prediction of binding mode and affinity. Recently Milletti et al have shown that using the most stable predicted tautomeric form in water for virtual screening significantly improves results over using the unstable tautomer (J Chem Inf Model 2010,50:1062-1074). MoKa 2.0 contains a number of key enhancements over MoKa 1.0. - Some ionizable centres not identified by MoKa 1.0 have now been added (the total number of predicted centres is now 106) - The number of models describing the chemical space has been expanded from 35 to 53. - Hundreds of molecules have been synthesized and experimentally tested to improve the training of a number of models - Some models in MoKa 1.0 were found to display an overfitting effect; this has now been fixed improving these models' external predictivity. - Tautomer enumeration is now quasi-exhaustive, and also independent of the input tautomer. - Model training has been improved, highlighting the impact of user data on the built-in models. - The analysis of experimental pKa versus predicted values has been improved, making it easier to focus on any poorly predicted compounds. - Redundant protomer enumeration is now allowed as an optional argument, so that both protonation states are produced when there are wo ionization states with a close predicted pKa difference - On an external Roche dataset of about 14,000 compounds, with 18500 pKa values, the MoKa 2.0 standard error was 0.50 log units Additional features include: - logP/logD prediction - Pipeline Pilot bindings for pKa prediction, protonation state enumeration and tautomer enumeration MoKa 2.0 is available for both Windows and Linux platforms. More information can be found here: http://www.moldiscovery.com/soft_moka.php Kind regards, Martin Dr. Martin Bohl Commercial Director Molecular Discovery Ltd Email: martin[at]moldiscovery[dot]com Molecular Discovery provides robust, high-quality and innovative computational methods addressing pharmaceutical needs in the field of drug discovery, including methods for virtual screening, lead optimisation, ADME modelling and metabolism research. Molecular Discovery software products offer calculation of accurate Molecular Interaction Fields for structure-based design (GRID), ligand-based and structure-based virtual screening (FLAP), pharmacophore elucidation (FLAP), metabolism prediction (MetaSite), metabolite identification (Mass-MetaSite), scaffold hopping (SHOP), pKa prediction (MoKa), 3D-QSAR modeling (FLAP, Pentacle) to improve efficiency in modern drug discovery. More information can be found on the main page: http://www.moldiscovery.com/ From owner-chemistry@ccl.net Thu Jan 10 16:16:00 2013 From: "Daniele Gianni daniele.gianni##gmail.com" To: CCL Subject: CCL: 2013 Workshop on Interoperability in Scientific Computing **FINAL ... Message-Id: <-48052-130110151244-26383-kBcj5DeJaf8KcqDlvBZjuQ|*|server.ccl.net> X-Original-From: Daniele Gianni Content-Type: multipart/alternative; boundary=e89a8f23501dc5c87804d2f4cc59 Date: Thu, 10 Jan 2013 21:12:36 +0100 MIME-Version: 1.0 Sent to CCL by: Daniele Gianni [daniele.gianni{=}gmail.com] --e89a8f23501dc5c87804d2f4cc59 Content-Type: text/plain; charset=ISO-8859-1 2013 Workshop on Interoperability in Scientific Computing **FINAL CALL FOR PAPERS - SUBMISSION DEADLINE 20th JANUARY 2013** ======================================================================== In conjunction with ICCS 2013 June 5-7 2013, Barcelona, Spain. http://www.cs.ox.ac.uk/david.johnson/wisc13/ The 13th annual International Conference on Computational Science (ICCS 2013) will be held in Barcelona, Spain from 5th - 7th June 2013. ICCS is an ERA 2010 'A'-ranked conference series. For more details on the main conference, please visit www.iccs-meeting.org The 2nd Workshop on Interoperability in Scientific Computing (WISC '13) will be co-located with ICCS 2013. Approaches to modelling take many forms. The mathematical, computational and encapsulated components of models can be diverse in terms of complexity and scale, as well as in published implementation (mathematics, source code, and executable files). Many of these systems are attempting to solve real-world problems in isolation. However the long-term scientific interest is in allowing greater access to models and their data, and to enable simulations to be combined in order to address ever more complex issues. Markup languages, metadata specifications, and ontologies for different scientific domains have emerged as pathways to greater interoperability. Domain specific modelling languages allow for a declarative development process to be achieved. Metadata specifications enable coupling while ontologies allow cross platform integration of data. The goal of this workshop is to bring together researchers from across scientific disciplines whose computational models require interoperability. This may arise through interactions between different domains, systems being modelled, connecting model repositories, or coupling models themselves, for instance in multi-scale or hybrid simulations. The outcomes of this workshop will be to better understand the nature of multidisciplinary computational modelling and data handling. Moreover we hope to identify common abstractions and cross-cutting themes in future interoperability research applied to the broader domain of scientific computing. The first instance of this workshop (WISC '11) was successfully held as part of the IEEE eScience conference in 2011 in Stockholm, Sweden, where all accepted papers were published in the workshops proceedings by the IEEE Computer Society and archived on IEEE eXplore. We look forward to your contributions and participation in WISC '13. **FINAL CALL FOR PAPER SUBMISSIONS** We invite submissions for high-quality papers (up to 10 pages in length) within the context of scientific computing in any of the traditional sciences (physics, chemistry, biology), engineering, or scientific/mathematical modelling applied to the social sciences and humanities. Papers should address progress, results or positions in one or more of the following areas: * Use of metadata standards for annotating scientific models and data. * Curating and publishing digital models and data to online repositories. * Meta-modelling and markup languages for model description. * Theoretical frameworks for combining disparate models, multi-scale models. * Using standardised data formats in computational models. * Domain-specific ontologies for the sciences. Proceedings of the ICCS 2013 workshops will be published by Elsevier Science, and will be made available online through the open-access Procedia Computer Science. Selected papers from the conference will be considered for publication in Elsevier's Journal of Computational Science. SUBMISSION PROCESS Authors are invited to submit papers with unpublished, original work of not more than 10 pages, as per the rules of Procedia Computer Science. Selected papers from the conference will be considered for publication in Elsevier's Journal of Computational Science. Templates are available from here: LaTeX template: http://www.iccs-meeting.org/iccs2013/procedia/ecrc-procs.zip MS Word template: http://www.iccs-meeting.org/iccs2013/procedia/ProcediaComputerScience_template.dot Papers conforming to the above guidelines should be submitted through the ICCS online submission system here: http://www.iccs-meeting.org/iccs2013/papers/upload.php Note, when submitting your paper please be sure to select the correct workshop, otherwise it will not be directed to the workshop organisers. It is expected that at least one author of each accepted paper attend the conference and workshop. IMPORTANT DATES Full papers due: **EXTENDED TO 20th JANUARY 2013** Notification of acceptance: 10th February 2013 Camera-ready: 1st March 2013 Workshop date: TBC, June 2013 CHAIRS/ORGANISERS David Johnson (University of Oxford, UK) Steve McKeever (Uppsala University, Sweden) Contact: david.johnson~~cs.ox.ac.uk --e89a8f23501dc5c87804d2f4cc59 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
2013 Workshop on Interoperability in Scientific Computing
**= FINAL CALL FOR PAPERS - SUBMISSION DEADLINE 20th JANUARY 2013**
= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
In conjunction with ICCS 2013 June 5-7 2013, Barcelona, Spain.
http://www.cs.o= x.ac.uk/david.johnson/wisc13/

The 13th annual = International Conference on Computational Science (ICCS 2013)=A0
will be held in Barcelona, Spain from 5th - 7th June 2013. ICCS is an = ERA 2010
'A'-ranked conference series. For more details o= n the main conference, please
visit www.iccs-meeting.org The 2nd Workshop on Interoperability in= Scientific
Computing (WISC '13) will be co-located with ICCS 2013.
=
Approaches to modelling take many forms. The mathematical, c= omputational and=A0
encapsulated components of models can be dive= rse in terms of complexity and=A0
scale, as well as in published implementation (mathematics, source cod= e, and=A0
executable files). Many of these systems are attempting= to solve real-world=A0
problems in isolation. However the long-t= erm scientific interest is in allowing=A0
greater access to models and their data, and to enable simulations to = be combined=A0
in order to address ever more complex issues. Mark= up languages, metadata=A0
specifications, and ontologies for diff= erent scientific domains have emerged as=A0
pathways to greater interoperability. Domain specific modelling langua= ges allow=A0
for a declarative development process to be achieved= . Metadata specifications=A0
enable coupling while ontologies all= ow cross platform integration of data.

The goal of this workshop is to bring together research= ers from across scientific=A0
disciplines whose computational mod= els require interoperability. This may arise=A0
through interacti= ons between different domains, systems being modelled, connecting=A0
model repositories, or coupling models themselves, for instance in mul= ti-scale or=A0
hybrid simulations. The outcomes of this workshop = will be to better understand the=A0
nature of multidisciplinary c= omputational modelling and data handling. Moreover we=A0
hope to identify common abstractions and cross-cutting themes in futur= e=A0
interoperability research applied to the broader domain of s= cientific computing.

The first instance of this wo= rkshop (WISC '11) was successfully held as part of=A0
the IEEE eScience conference in 2011 in Stockholm, Sweden, where all a= ccepted papers=A0
were published in the workshops proceedings by = the IEEE Computer Society and=A0
archived on IEEE eXplore. We loo= k forward to your contributions and participation=A0
in WISC '13.

**FINAL CALL FOR PAPER SUBMI= SSIONS**

We invite submissions for high-quality pa= pers (up to 10 pages in length) within=A0
the context of scientif= ic computing in any of the traditional sciences (physics,=A0
chemistry, biology), engineering, or scientific/mathematical modelling= applied to=A0
the social sciences and humanities. Papers should = address progress, results or=A0
positions in one or more of the f= ollowing areas:

* Use of metadata standards for annotating scientific m= odels and data.
* Curating and publishing digital models and data= to online repositories.
* Meta-modelling and markup languages fo= r model description.
* Theoretical frameworks for combining disparate models, multi-scale m= odels.
* Using standardised data formats in computational models.=
* Domain-specific ontologies for the sciences.

Proceedings of the ICCS 2013 workshops will be published by Else= vier Science, and=A0
will be made available online through the op= en-access Procedia Computer Science.=A0
Selected papers from the = conference will be considered for publication in=A0
Elsevier's Journal of Computational Science.

<= div>SUBMISSION PROCESS

Authors are invited to subm= it papers with unpublished, original work of not more=A0
than 10 = pages, as per the rules of Procedia Computer Science. Selected papers from= =A0
the conference will be considered for publication in Elsevier's Jo= urnal of=A0
Computational Science.

Templ= ates are available from here:


MS Word template:=A0

Papers conforming to the above guidelines should be sub= mitted through the ICCS=A0
online submission system here:


Note, when submitting your paper please be sure to sele= ct the correct workshop,=A0
otherwise it will not be directed to = the workshop organisers.

It is expected that at le= ast one author of each accepted paper attend the conference=A0
and workshop.

IMPORTANT DATES

<= /div>
Full papers due: **EXTENDED TO 20th JANUARY 2013**
Noti= fication of acceptance: 10th February 2013
Camera-ready: 1st Marc= h 2013
Workshop date: TBC, June 2013

CHAIRS/ORGANISE= RS

David Johnson (University of Oxford, UK)
<= div>Steve McKeever (Uppsala University, Sweden)

--e89a8f23501dc5c87804d2f4cc59-- From owner-chemistry@ccl.net Thu Jan 10 16:51:00 2013 From: "Y. Yuan echemistry**yahoo.com" To: CCL Subject: CCL: TouchMol for Microsoft Office 1.1 Release Message-Id: <-48053-130110163039-18700-quXDoKIT0lD9i1OBw+XIBg-.-server.ccl.net> X-Original-From: "Y. Yuan" Content-Type: multipart/alternative; boundary="275539708-1279200962-1357853432=:71155" Date: Thu, 10 Jan 2013 13:30:32 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Y. Yuan" [echemistry:_:yahoo.com] --275539708-1279200962-1357853432=:71155 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Scilligence=C2=A0is very pleased to announce the release of TouchMol for MS= Office version 1.1. =C2=A0=C2=A0TouchMol for Office is delivered as a set = of add-ins to the Microsoft Office application programs.=C2=A0 Enabling the= input and editing of molecular structures within Word, Excel, PowerPoint, = and OneNote.=0ATouchMol 1.1 includes the following new features:=0ATouchMol= .Table =E2=80=93 A new component to TouchMol for Office introduced in this = version that can:=0A=091. Open/Save SDF, CSV, MolEngine files=0A=092. Displ= ay Data in Table and Grid mode=0A=093. Color coding of cells for heat maps= =0A=094. Fast structure search=0A=095. Structure duplicate checking=0A=096.= Query the PubChem database for Patent, Assay, and Literature data=0A=097. = Load data or calculates properties from databases and web services=0A=098. = Configure GUI to query in-house databases, including SQL Server, Oracle and= MySql=0A=099. Calculate properties locally with MolEngine=0A=0910. Flag an= d categorize=C2=A0 compounds=0ATouchMol Application=0A=091. Generate IUPAC = names from variety of structure-to-name module=0A=092. Look up IUPAC names = > from PubChem and ChemSpider databases=0ATouchMol for Excel=0A=091. Open/exp= ort CSV and MolEngine files=0A=092. Load and filter large compound library = via TouchMol.Table=0A=093. Query PubChem database for Patent, Assay and Lit= erature data=0A=094. Load data from databases or web services=0A=095. Confi= gure GUI to query in-house databases, including SQL Server, Oracle and MySq= l=0A=096. Calculate properties locally with MolEngine, or remotely calling = web services=0ATouchMol for Word=0A=091. Generate IUPAC names using structu= re-to-name module=0A=092. Look up IUPAC names from PubChem and ChemSpider d= atabases=0ATo download our Preview of TouchMol 1.1, follow the links below:= =0ATouchMol for Office 2010 (for both x86 and x64):=0Ahttp://www.scilligenc= e.com/web/download.aspx?prod=3DTouchMol4Office2010=0ATouchMol for Office 20= 07:=0Ahttp://www.scilligence.com/web/download.aspx?prod=3DTouchMol4Office20= 07=0A=0AScilligence --275539708-1279200962-1357853432=:71155 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Scilligence is very pleased to ann= ounce the release of TouchMol for MS Office version 1.1.   TouchM= ol for Office is delivered as a set of add-ins to the Microsoft Office appl= ication programs.  Enabling the input and editing of molecular structu= res within Word, Excel, PowerPoint, and OneNote.
TouchMol 1.1 includes the following new features:
TouchMol.Table =E2=80=93 A new component to Tou= chMol for Office introduced in this version that can:
  1. Open= /Save SDF, CSV, MolEngine files
  2. Display Data in Table and Grid mode
  3. Color coding of cells for heat maps
  4. Fast structure search
  5. Structure duplicate checking
  6. Query the PubChem database for Patent, A= ssay, and Literature data
  7. Configure GUI to query in-house databases, i= ncluding SQL Server, Oracle and MySql
  8. Calculate properties locally with MolEngine
  9. Flag and categorize  compounds
    10. <= /ol>
    TouchMol Application
    1. Generate IUPAC names from variety of structure-to-name module
    2. Look up IUPAC names from PubChem a= nd ChemSpider databases
    TouchMol = for Excel
    1. Open/export CSV and MolEngine files
    2. Load and filter large compound libra= ry via TouchMol.Table
    3. Qu= ery PubChem database for Patent, Assay and Literature data
    4. Load data from databases or web services=
    5. Configure GUI to query = in-house databases, including SQL Server, Oracle and MySql
    6. Calculate properties locally with MolEngine, or = remotely calling web services
    T= ouchMol for Word
    1. Generate IUPAC names using structure-to-n= ame module
    2. Look up IUPAC= names from PubChem and ChemSpider databases
    To download our Preview of TouchMol 1.1, follow the links below:

    Scilligence
--275539708-1279200962-1357853432=:71155--